LAMMPS (28 Mar 2023 - Development)
  using 1 OpenMP thread(s) per MPI task
# 3d rounded cubes

variable    r     index 3
variable    steps index 10000

units       lj
dimension   3

atom_style  body rounded/polyhedron 1 10

read_data   data.cubes
Reading data file ...
  orthogonal box = (0 0 0) to (6 6 6)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2 atoms
  2 bodies
  read_data CPU = 0.001 seconds

replicate   $r $r $r
replicate   3 $r $r
replicate   3 3 $r
replicate   3 3 3
Replication is creating a 3x3x3 = 27 times larger system...
  orthogonal box = (0 0 0) to (18 18 18)
  1 by 1 by 1 MPI processor grid
  54 atoms
  replicate CPU = 0.001 seconds

velocity    all create 1.2 187287 dist gaussian mom yes rot yes

variable cut_inner  equal 0.5
variable k_n        equal 100
variable k_na       equal 1
variable c_n        equal 20
variable c_t        equal 5
variable mu         equal 0
variable A_ua       equal 1

pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner}
pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner}
pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner}
pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner}
pair_style body/rounded/polyhedron 20 5 0 1 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 1

comm_modify vel yes

neighbor     0.5 bin
neigh_modify every 1 delay 0 check yes

timestep     0.001

#fix          1 all nve/body
fix          1 all nvt/body temp 1.2 1.2 0.1
#fix          1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0

compute      p2 all pressure 1_temp

#compute      1 all body/local id 1 2 3
#dump         1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4]

#dump         2 all image 1000 image.*.jpg type type #             zoom 1.5 adiam 1.5 body type 0 0 view 60 15
#dump_modify  2 pad 6

thermo_style custom step ke pe etotal c_p2 c_1_temp

thermo       1000

run          ${steps}
run          10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.9641016
  ghost atom cutoff = 3.9641016
  binsize = 1.9820508, bins = 10 10 10
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair body/rounded/polyhedron, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.973 | 5.973 | 5.973 Mbytes
   Step         KinEng         PotEng         TotEng          c_p2         c_1_temp   
         0   1.7666667      0              1.7666667      0.01090535     0.59439252   
      1000   3.1462962      0.17392649     3.3202227      0.02361912     1.1654694    
      2000   2.9311648      0.13836102     3.0695258      0.021748224    1.1950624    
      3000   3.090491       0.16511199     3.255603       0.018691142    1.23672      
      4000   2.7401565      0.17792155     2.9180781      0.015093853    1.1180839    
      5000   3.0880849      0.17587085     3.2639557      0.030563042    1.2831154    
      6000   3.2180776      0.19732251     3.4154001      0.028338151    1.258839     
      7000   2.9514882      0.25088882     3.202377       0.025296925    1.1746326    
      8000   3.0101226      0.28825968     3.2983823      0.027273454    1.2138056    
      9000   3.0164253      0.1901733      3.2065986      0.033228915    1.3095914    
     10000   2.3780401      0.34082434     2.7188644      0.031838531    1.0208679    
Loop time of 33.0201 on 1 procs for 10000 steps with 54 atoms

Performance: 26165.890 tau/day, 302.846 timesteps/s, 16.354 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 32.897     | 32.897     | 32.897     |   0.0 | 99.63
Neigh   | 0.0028124  | 0.0028124  | 0.0028124  |   0.0 |  0.01
Comm    | 0.034404   | 0.034404   | 0.034404   |   0.0 |  0.10
Output  | 0.00017643 | 0.00017643 | 0.00017643 |   0.0 |  0.00
Modify  | 0.078202   | 0.078202   | 0.078202   |   0.0 |  0.24
Other   |            | 0.00767    |            |       |  0.02

Nlocal:             54 ave          54 max          54 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             96 ave          96 max          96 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            100 ave         100 max         100 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 100
Ave neighs/atom = 1.8518519
Neighbor list builds = 268
Dangerous builds = 0

Total wall time: 0:00:33
